source: cpp/frams/genetics/genman.cpp @ 757

// This file is a part of Framsticks SDK.  http://www.framsticks.com/
// Copyright (C) 1999-2015  Maciej Komosinski and Szymon Ulatowski.
// See LICENSE.txt for details.

#include "genman.h"
#include <frams/vm/classes/genoobj.h>
#include GEN_CONFIG_FILE //configuration of active genetic operators
#include "common/log.h"
#include "common/nonstd_math.h"
#include "common/stl-util.h"
#include <common/loggers/loggers.h>


#ifdef USE_GENMAN_f0
#include "f0/oper_f0.h"
#endif
#ifdef USE_GENMAN_f0FUZZY
#include "f0/oper_f0Fuzzy.h"
#endif
#ifdef USE_GENMAN_f1
#include "f1/oper_f1.h"
#endif
#ifdef USE_GENMAN_f2
#include "f2/oper_f2.h"
#endif
#ifdef USE_GENMAN_f2
#include "f3/oper_f3.h"
#endif
#ifdef USE_GENMAN_f4
#include "f4/oper_f4.h"
#endif
#ifdef USE_GENMAN_f5
#include "f5/oper_f5.h"
#endif
#ifdef USE_GENMAN_f6
#include "f6/oper_f6.h"
#endif
#ifdef USE_GENMAN_f7
#include "f7/oper_f7.h"
#endif
#ifdef USE_GENMAN_f8
#include "f8/oper_f8.h"
#endif
#ifdef USE_GENMAN_f9
#include "f9/oper_f9.h"
#endif
#ifdef USE_GENMAN_fF
#include "fF/oper_fF.h"
#endif
#ifdef USE_GENMAN_fn
#include "fn/oper_fn.h"
#endif
#ifdef USE_GENMAN_fT
#include "fT/oper_fTest.h"
#endif

using namespace std; //string, vector

//old code needs update:
//#include "gengroups.h"
//extern GenGroup *listaGen;
//   GENGROUP(0)->l_del.add(sim->GM.onDelGen,&sim->GM); //before delete
//   GENGROUP(0)->l_del.remove(sim->GM.onDelGen,&sim->GM); //before delete


#define FIELDSTRUCT GenMan

static ParamEntry GMparam_tab[] =
{
        { "Genetics", 1, 10, "GenMan", },
        { "gen_hist", 0, PARAM_DONTSAVE, "Remember history of genetic operations", "d 0 1 0", FIELD(history), "Required for phylogenetic analysis", },
        { "gen_hilite", 0, 0, "Use syntax highlighting", "d 0 1 1", FIELD(hilite), "Use colors for genes?\n(slows down viewing/editing of huge genotypes)", },
        { "gen_extmutinfo", 0, 0, "Extended mutation info", "d 0 2 0 ~Off~Method ID~Method description", FIELD(extmutinfo), "If active, information about employed mutation method will be stored in the 'info' field of each mutated genotype.", },
        { "operReport", 0, PARAM_DONTSAVE, "Operators report", "p()", PROCEDURE(p_report), "Show available genetic operators", },
        { "toHTML", 0, PARAM_DONTSAVE, "HTMLize a genotype", "p s(s)", PROCEDURE(p_htmlize), "returns genotype expressed as colored HTML", },
        { "toHTMLshort", 0, PARAM_DONTSAVE, "HTMLize a genotype, shorten if needed", "p s(s)", PROCEDURE(p_htmlizeshort), "returns genotype (abbreviated if needed) expressed as colored HTML", },
        { "validate", 0, PARAM_DONTSAVE | PARAM_USERHIDDEN, "Validate", "p oGeno(oGeno)", PROCEDURE(p_validate), "returns validated (if possible) Geno object from supplied Geno", },
        { "mutate", 0, PARAM_DONTSAVE | PARAM_USERHIDDEN, "Mutate", "p oGeno(oGeno)", PROCEDURE(p_mutate), "returns mutated Geno object from supplied Geno", },
        { "crossOver", 0, PARAM_DONTSAVE | PARAM_USERHIDDEN, "Crossover", "p oGeno(oGeno,oGeno)", PROCEDURE(p_crossover), "returns crossed over genotype", },
        { "getSimplest", 0, PARAM_DONTSAVE | PARAM_USERHIDDEN, "Get simplest genotype", "p oGeno(s format)", PROCEDURE(p_getsimplest), "returns the simplest genotype for a given encoding (format). \"0\" means f0, \"4\" means f4, etc.", },
        { 0, },
};

static ParamEntry GMstats_tab[] =
{
        { "Genetics", 1, 12, "GenManStats", "Statistics for genetic operations." },
        { "gen_count", 0, PARAM_READONLY, "Number of genetic operations so far", "d", FIELD(count), "", },
        { "gen_mvalid", 0, PARAM_READONLY, "Mutations valid", "d", FIELD(valid_m), "", },
        { "gen_mvalidated", 0, PARAM_READONLY, "Mutations validated", "d", FIELD(validated_m), "", },
        { "gen_minvalid", 0, PARAM_READONLY, "Mutations invalid", "d", FIELD(invalid_m), "couldn't be repaired", },
        { "gen_mfailed", 0, PARAM_READONLY, "Mutations failed", "d", FIELD(failed_m), "couldn't be performed", },
        { "gen_xovalid", 0, PARAM_READONLY, "Crossovers valid", "d", FIELD(valid_xo), "", },
        { "gen_xovalidated", 0, PARAM_READONLY, "Crossovers validated", "d", FIELD(validated_xo), "", },
        { "gen_xoinvalid", 0, PARAM_READONLY, "Crossovers invalid", "d", FIELD(invalid_xo), "couldn't be repaired", },
        { "gen_xofailed", 0, PARAM_READONLY, "Crossovers failed", "d", FIELD(failed_xo), "couldn't be performed", },
        { "gen_mutimpr", 0, PARAM_READONLY, "Mutations total effect", "f", FIELD(mutchg), "total cumulative mutation change", },
        { "gen_xoimpr", 0, PARAM_READONLY, "Crossovers total effect", "f", FIELD(xochg), "total cumulative crossover change", },
        { "clrstats", 0, PARAM_DONTSAVE, "Clear stats and history", "p()", PROCEDURE(p_clearStats), "", },
        { 0, },
};

#undef FIELDSTRUCT

GenMan::GenMan() : localpar(GMparam_tab, this), localstats(GMstats_tab, this),
seloperpar("GenOperators", "Genetics: Active operators"),
neuronsparam("Genetics: Neurons to add", "neuronsAdd", "neuadd_"),
par("GenMan", "Manages various genetic operations, using appropriate operators for the argument genotype format.")
{
        history = 0;
        hilite = 1;
        clearStats();

#ifdef USE_GENMAN_f0
        oper_fx_list.push_back(new Geno_f0);
#endif
#ifdef USE_GENMAN_f0FUZZY
        oper_fx_list.push_back(new Geno_f0Fuzzy);
#endif
#ifdef USE_GENMAN_f1
        oper_fx_list.push_back(new Geno_f1);
#endif
#ifdef USE_GENMAN_f2
        oper_fx_list.push_back(new Geno_f2);
#endif
#ifdef USE_GENMAN_f3
        oper_fx_list.push_back(new Geno_f3);
#endif
#ifdef USE_GENMAN_f4
        oper_fx_list.push_back(new Geno_f4);
#endif
#ifdef USE_GENMAN_f5
        oper_fx_list.push_back(new Geno_f5);
#endif
#ifdef USE_GENMAN_f6
        oper_fx_list.push_back(new Geno_f6);
#endif
#ifdef USE_GENMAN_f7
        oper_fx_list.push_back(new Geno_f7);
#endif
#ifdef USE_GENMAN_f8
        oper_fx_list.push_back(new Geno_f8);
#endif
#ifdef USE_GENMAN_f9
        oper_fx_list.push_back(new GenoOper_f9);
#endif
#ifdef USE_GENMAN_fF
        oper_fx_list.push_back(new GenoOper_fF);
#endif
#ifdef USE_GENMAN_fn
        oper_fx_list.push_back(new GenoOper_fn);
#endif
#ifdef USE_GENMAN_fT
        oper_fx_list.push_back(new GenoOper_fTest);
#endif

        seloper = new int[oper_fx_list.size()]; //may result in a little overhead if some of the operators on the oper_fx_list concern the same genetic format
        int selopercount = 0;
        for (unsigned int i = 0; i < oper_fx_list.size(); i++)
        {
                if (operformats.find(oper_fx_list[i]->supported_format) != -1) continue;
                string type = string("~") + oper_fx_list[i]->name;
                int dup = 0;
                for (unsigned int j = i + 1; j < oper_fx_list.size(); j++)
                        if (oper_fx_list[i]->supported_format == oper_fx_list[j]->supported_format)
                        {
                                type += "~";
                                type += oper_fx_list[j]->name;
                                dup++;
                        }
                type = ssprintf("d 0 %d ", dup) + type;
                string id = ssprintf("genoper_f%c", oper_fx_list[i]->supported_format);
                string name = ssprintf("Operators for f%c", oper_fx_list[i]->supported_format);
                seloper[selopercount] = 0;
                operformats += oper_fx_list[i]->supported_format;
                //printf("%x %s %s %s\n",&seloper[selopercount],(const char*)id,(const char*)type,(const char*)name);
                seloperpar.addProperty(&seloper[selopercount++], id.c_str(), type.c_str(), name.c_str(), "", PARAM_READONLY*(dup == 0));
        }

        par += &localpar;
        par += &seloperpar;
        par += &neuronsparam;
        for (unsigned int i = 0; i < oper_fx_list.size(); i++)
                if (oper_fx_list[i]->par.getParamTab()) par += &oper_fx_list[i]->par;

        setDefaults(); //use Param to initialize all values of fields in the paramtab of this object and genetic operators on oper_fx_list
}

GenMan::~GenMan()
{
        for (unsigned int i = 0; i < oper_fx_list.size(); i++) delete oper_fx_list[i];
        delete[] seloper;
}

void GenMan::setDefaults()
{
        for (unsigned int i = 0; i < oper_fx_list.size(); i++)
        {
                oper_fx_list[i]->par.setDefault();
                oper_fx_list[i]->setDefaults();
        }
        localpar.setDefault();
        //...and we do not reset others that are linked to 'par',
        //because there quite a few of them, and not every of them defines defaults for each of its parameters.
}

int GenMan::testValidity(Geno &g, bool &canvalidate)
{
        SString ggs=g.getGenes();
        const char *gg = ggs.c_str();
        GenoOperators *gf = getOper_f(g.getFormat());
        int check1;
        if (!gf) { canvalidate = false; return GENOPER_NOOPER; }
        else check1 = gf->checkValidity(gg,g.getName().c_str());
        if (!canvalidate) return check1; //just checking
        if (check1 == GENOPER_OK) { canvalidate = false; return check1; }
        char *g2 = strdup(gg);
        if (gf->validate(g2,g.getName().c_str()) == GENOPER_NOOPER) { free(g2); canvalidate = false; return check1; }
        if (check1 == GENOPER_NOOPER) //disaster: cannot check because there is no check operator
        {
                g.setGenesAssumingSameFormat(g2); free(g2); canvalidate = false; return GENOPER_NOOPER;
        }
        int check2 = gf->checkValidity(g2, "validated");
        if (check2 == GENOPER_OK) g.setGenesAssumingSameFormat(g2);
        free(g2);
        if (check2 == GENOPER_OK) return check1;
        canvalidate = false;
        return check1; //could not validate.
}

int GenMan::testGenoValidity(Geno& g)
{
        bool fix = false;
        switch (testValidity(g, fix))
        {
        case GENOPER_OK: return 1;
        case GENOPER_NOOPER: return -1;
        default: return 0;
        }
}

Geno GenMan::validate(const Geno& geny)
{
        char format = geny.getFormat();
        GenoOperators *gf = getOper_f(format);
        if (gf == NULL)
                return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: Validate(): don't know how to handle genetic format %c", format));
        char *g2 = strdup(geny.getGenes().c_str()); //copy for validation
        int res = gf->validate(g2, geny.getName().c_str());
        SString sg2 = g2;
        free(g2);
        if (res == GENOPER_OK)
                return Geno(sg2, format, geny.getName(), geny.getComment());
        else
                return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: validate() for format %c returned invalid value", format));
}

Geno GenMan::mutate(const Geno& g)
{
        float chg; //how many changes
        int method; //mutation method
        char format = g.getFormat();
        GenoOperators *gf = getOper_f(format);
        if (gf == NULL)
                return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: Mutate(): don't know how to handle genetic format %c", format));
        Geno gv = g;
        bool canvalidate = true;
        if (testValidity(gv, canvalidate) > 0 && canvalidate == false)
                return Geno("", -1, "", "GENOPER_OPFAIL: Mutate(): cannot validate invalid source genotype");
        bool ok = false;
        int pcount = count;
        while (!ok)
        {
                char *gn = strdup(gv.getGenes().c_str()); //copy for mutation
                chg = 0;
                if (gf->mutate(gn, chg, method) == GENOPER_OK)
                {
                        LoggerToMemory eh(LoggerBase::Enable | LoggerToMemory::StoreFirstMessage); //mute testValidity()
                        Geno G(gn, gv.getFormat(), "", "");
                        canvalidate = true;
                        int res = testValidity(G, canvalidate);
                        if (res == GENOPER_OK && canvalidate == false) { valid_m++; ok = true; }
                        else
                                if (res > 0 && canvalidate == false) invalid_m++; else
                                {
                                        validated_m++; ok = true;
                                }
                        if (ok) gv = G;
                }
                else failed_m++;
                free(gn);
                count++;
                if (!ok && (count - pcount > 100))
                {
                        logPrintf("GenMan", "Mutate", 2, "Tried 100x and failed: %s", g.getGenes().c_str());
                        return Geno("", -1, "", "GENOPER_OPFAIL: Mutate() tried 100x and failed");
                }
        }
        mutchg += chg;
        if (history) saveLink(g.getGenes().c_str(), "", gv.getGenes().c_str(), chg);
        SString mutinfo;
        if (extmutinfo == 0) mutinfo = SString::sprintf("%.2f%% mutation of '%s'", 100 * chg, g.getName().c_str()); else
                if (extmutinfo == 1) mutinfo = SString::sprintf("%.2f%% mutation(%d) of '%s'", 100 * chg, method, g.getName().c_str()); else
                        mutinfo = SString::sprintf("%.2f%% mutation(%s) of '%s'", 100 * chg, gf->mutation_method_names ? gf->mutation_method_names[method] : "unspecified method name", g.getName().c_str());
        gv.setComment(mutinfo);
        return gv;
}

Geno GenMan::crossOver(const Geno& g1, const Geno& g2)
{
        char format = g1.getFormat();
        if (format != g2.getFormat()) return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: CrossOver(): does not work for parents with differing genetic formats (%c and %c)", format, g2.getFormat()));
        GenoOperators *gf = getOper_f(format);
        if (gf == NULL)
                return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: CrossOver(): no operators found for genetic format %c", format));
        Geno g1v = g1, g2v = g2;

        {
                LoggerToMemory eh(LoggerBase::Enable | LoggerToMemory::StoreFirstMessage); //mute testValidity()
                bool canvalidate = true;
                if (testValidity(g1v, canvalidate) > 0 && canvalidate == false)
                        return Geno("", -1, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #1");
                canvalidate = true;
                if (testValidity(g2v, canvalidate) > 0 && canvalidate == false)
                        return Geno("", -1, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #2");
        }

        float chg;
        bool ok = false;
        int pcount = count;

        while (!ok)
        {
                float chg1, chg2;
                char *g1n = strdup(g1.getGenes().c_str()); //copy for crossover
                char *g2n = strdup(g2.getGenes().c_str()); //copy for crossover
                chg1 = chg2 = 0;
                if (gf->crossOver(g1n, g2n, chg1, chg2) == GENOPER_OK)
                {
                        char *gn;
                        if (g1n[0] && g2n[0]) if (randomN(2) == 0) g1n[0] = 0; else g2n[0] = 0; //both provided? we want only one
                        if (g1n[0]) { gn = g1n; chg = chg1; }
                        else { gn = g2n; chg = chg2; }
                        LoggerToMemory eh(LoggerBase::Enable | LoggerToMemory::StoreFirstMessage); //mute testValidity()
                        Geno G(gn, g1v.getFormat(), "", "");
                        bool canvalidate = true;
                        int res = testValidity(G, canvalidate);
                        if (res == GENOPER_OK && canvalidate == false) { valid_xo++; ok = true; }
                        else
                                if (res > 0 && canvalidate == false) invalid_xo++; else
                                {
                                        validated_xo++; ok = true;
                                }
                        if (ok) g1v = G;
                }
                else failed_xo++;
                free(g1n);
                free(g2n);
                count++;
                if (!ok && (count - pcount > 100))
                {
                        logPrintf("GenMan", "CrossOver", 2, "Tried 100x and failed: %s and %s", g1.getGenes().c_str(), g2.getGenes().c_str());
                        return Geno("", -1, "", "GENOPER_OPFAIL: CrossOver() tried 100x and failed");
                }
        }
        // result in g1v
        xochg += chg;
        if (history) saveLink(g1.getGenes().c_str(), g2.getGenes().c_str(), g1v.getGenes().c_str(), chg);
        SString xoinfo = SString::sprintf("Crossing over of '%s' (%.2f%%) and '%s' (%.2f%%)",
                g1.getName().c_str(), 100 * chg, g2.getName().c_str(), 100 * (1 - chg));
        g1v.setComment(xoinfo);
        return g1v;
}

float GenMan::similarity(const Geno& g1, const Geno& g2)
{
        char format = g1.getFormat();
        if (format != g2.getFormat()) return GENOPER_NOOPER;
        GenoOperators *gf = getOper_f(format);
        if (!gf) return GENOPER_NOOPER; else return gf->similarity(g1.getGenes().c_str(), g2.getGenes().c_str());
}

uint32_t GenMan::getStyle(const char *g, const Geno *G, int pos)
{
        char format = G->getFormat();
        if (format == Geno::INVALID_FORMAT)
                return GENSTYLE_RGBS(64, 64, 64, 0); // gray & "valid" (unknown format so we don't know what is valid and what is not)
        if ((pos = G->mapStringToGen(pos)) == -1) return GENSTYLE_COMMENT;
        GenoOperators *gf = getOper_f(format);
        if (!gf) return GENSTYLE_CS(0, 0); //black & valid
        else return gf->style(G->getGenes().c_str(), pos);
}

uint32_t GenMan::getStyle(const char *g, int pos)
{
        Geno G(g);
        return getStyle(g, &G, pos);
}

void GenMan::getFullStyle(const char *g, const Geno *G, uint32_t *styletab)
{
        char format = G->getFormat();
        if (format == Geno::INVALID_FORMAT)
        {
                for (unsigned int pos = 0; pos < strlen(g); pos++)
                        styletab[pos] = GENSTYLE_RGBS(64, 64, 64, 0); // gray & "valid" (unknown format so we don't know what is valid and what is not)
                return;
        }
        GenoOperators *gf = getOper_f(format);
        SString geny=G->getGenes();
        for (unsigned int pos = 0; pos < strlen(g); pos++)
        {
                int posmapped = G->mapStringToGen(pos);
                if (posmapped == -1) styletab[pos] = GENSTYLE_COMMENT;
                else if (!gf) styletab[pos] = GENSTYLE_CS(0, 0); //black & valid
                else styletab[pos] = gf->style(geny.c_str(), posmapped);
                //logPrintf("GenMan", "getFullStyle", 0, "%d  char='%c' (%d)  format=0x%08x", pos, g[pos], g[pos], styletab[pos]);
        }
}

void GenMan::getFullStyle(const char *g, uint32_t *styletab)
{
        Geno G(g);
        getFullStyle(g, &G, styletab);
}

string GenMan::HTMLize(const char *g) { return HTMLize(g, false); }

string GenMan::HTMLizeShort(const char *g) { return HTMLize(g, true); }

string GenMan::HTMLize(const char *g, bool shorten)
{
        char buf[50];
        int len = strlen(g);
        int chars = 0, lines = 0;
        bool shortened = false;
        uint32_t *styletab = new uint32_t[len];
        getFullStyle(g, styletab);
        string html = "\n<div style=\"background:white;padding:0.2em;font-family:arial,helvetica,sans-serif;font-size:90%\">";
        uint32_t prevstyle, prevcolor, style = 0, color = 0;
        for (int i = 0; i<len; i++)
        {
                if (shorten && ((lines == 0 && chars>160) || (lines > 5 || chars > 300))) { shortened = true; break; }
                if (g[i] == '\r') continue;
                if (g[i] == '\n') { html += "<br>\n"; lines++; continue; }
                chars++;
                prevstyle = style;
                prevcolor = color;
                style = GENGETSTYLE(styletab[i]);
                color = GENGETCOLOR(styletab[i]);
                if ((i != 0 && (color != prevcolor))) html += "</font>";
                if ((style&GENSTYLE_INVALID) != (prevstyle&GENSTYLE_INVALID))
                {
                        html += "<"; if (!(style&GENSTYLE_INVALID)) html += "/"; html += "u>";
                }
                if ((style&GENSTYLE_BOLD) != (prevstyle&GENSTYLE_BOLD))
                {
                        html += "<"; if (!(style&GENSTYLE_BOLD)) html += "/"; html += "b>";
                }
                if ((style&GENSTYLE_ITALIC) != (prevstyle&GENSTYLE_ITALIC))
                {
                        html += "<"; if (!(style&GENSTYLE_ITALIC)) html += "/"; html += "i>";
                }
                if ((i == 0 || (color != prevcolor)))
                {
                        sprintf(buf, "<font color=#%02x%02x%02x>", GENGET_R(color), GENGET_G(color), GENGET_B(color)); html += buf;
                }
                if (g[i] == '<') html += "&lt;"; else if (g[i] == '>') html += "&gt;"; else html += g[i];
                if ((i % 3) == 0 && g[i] == ' ') html += "\n"; //for readability, insert some newlines into html...
        }
        delete[] styletab;
        html += "</u></b></i></font>";
        if (shortened) html += " [etc...]";
        html += "</div>\n";
        return html;
}

void GenMan::p_htmlize(ExtValue *args, ExtValue *ret)
{
        ret->setString(HTMLize(args->getString().c_str()).c_str());
}

void GenMan::p_htmlizeshort(ExtValue *args, ExtValue *ret)
{
        ret->setString(HTMLizeShort(args->getString().c_str()).c_str());
}

Geno GenMan::getSimplest(char format)
{
        GenoOperators *gf = getOper_f(format);
        if (!gf) return Geno();
        string info = "The simplest genotype of format f"; info += format;
        info += " for operators '"; info += gf->name; info += "'.";
        return Geno(gf->getSimplest(), format, "Root", info.c_str());
}

void GenMan::p_getsimplest(ExtValue *args, ExtValue *ret)
{
        int format = GenoObj::formatFromExtValue(args[0]);
        if (!getOper_f(format))
                ret->setEmpty();
        else
                *ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(getSimplest(format)));
}

const char *GenMan::getOpName(char format)
{
        GenoOperators *gf = getOper_f(format);
        if (!gf) return "n/a"; else return gf->name.c_str();
}

GenoOperators* GenMan::getOper_f(char format)
{
        int ind = operformats.find(format);
        if (ind == -1) return NULL;
        int which_oper_of_format = seloper[ind];
        for (unsigned int i = 0; i < oper_fx_list.size(); i++)
                if (oper_fx_list[i]->supported_format == format)
                        if (which_oper_of_format == 0) return oper_fx_list[i]; else which_oper_of_format--;
        return NULL; //should never happen
}

void GenMan::saveLink(const string parent1, const string parent2, const string child, const float chg)
{
        GenoLink l;
        l.count = count;
        l.parent1 = parent1;
        l.parent2 = parent2;
        l.child = child;
        l.chg = chg;
        l.fit = 0; //temporarily. Will be set when the genotype dies
        //logPrintf("GenMan","saveLink",0,"#%d: [%d] '%s' + '%s' -> '%s'",GenoLinkList.size(),count,parent1.c_str(),parent2.c_str(),child.c_str());
        GenoLinkList.push_back(l);
}

void GenMan::onDelGen(void *obj, intptr_t n)
{
        //old code needs update:
        //   ((SpeciesList*)obj)->przyDodaniu(i);
        /* !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
           GenMan *gm=(GenMan*)obj;
           Genotype *gt=(Genotype*)(*listaGen)(n); //there is no more "listaGen"
           string g=(const char*)gt->genotype.getGene();
           float fit=gt->getFinalFitness();
           for(int i=0;i<gm->GenoLinkList.size();i++) //find genotype
           if (gm->GenoLinkList[i].g1==g) {gm->GenoLinkList[i].fit=fit; break;}
           */
}

void GenMan::clearStats()
{
        count = 0;
        valid_m = valid_xo = validated_m = validated_xo = invalid_m = invalid_xo = failed_m = failed_xo = 0;
        mutchg = xochg = 0;
        GenoLinkList.clear();
}

void GenMan::p_clearStats(ExtValue *args, ExtValue *ret) { clearStats(); }

void GenMan::p_report(ExtValue *args, ExtValue *ret)
{                      //should be updated to handle multiple operators for a single format
        char *g, *g2;
        float f1, f2;
        int m;
        logMessage("GenMan", "Report", 0, "The following genetic operators are available:");
        for (unsigned int i = 0; i < oper_fx_list.size(); i++)
        {
                string l;
                if (oper_fx_list[i]->checkValidity("","") != GENOPER_NOOPER) l += " checkValidity";
                if (oper_fx_list[i]->getSimplest())
                {
                        g = strdup(oper_fx_list[i]->getSimplest());
                        g2 = strdup(g);
                        if (oper_fx_list[i]->validate(g,"") != GENOPER_NOOPER) l += " validate";
                        if (oper_fx_list[i]->mutate(g, f1, m) != GENOPER_NOOPER) l += " mutate";
                        if (oper_fx_list[i]->crossOver(g, g2, f1, f2) != GENOPER_NOOPER) l += " crossover";
                        l += " getSimplest";
                        free(g); free(g2);
                }
                //      if (oper_fx_list[i]->similarity("","")!=GENOPER_NOOPER) l+=" similarity";
                logPrintf("GenMan", "Report", 0, "format f%c (%s):%s",
                        oper_fx_list[i]->supported_format, oper_fx_list[i]->name.c_str(), l.c_str());
        }
}

void GenMan::p_validate(ExtValue *args, ExtValue *ret)
{
        Geno *g = GenoObj::fromObject(args[0]);
        if (g == NULL)
                ret->setEmpty();
        else
                *ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(validate(*g)));
}

void GenMan::p_mutate(ExtValue *args, ExtValue *ret)
{
        Geno *g = GenoObj::fromObject(args[0]);
        if (g == NULL)
                ret->setEmpty();
        else
                *ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(mutate(*g)));
}

void GenMan::p_crossover(ExtValue *args, ExtValue *ret)
{
        Geno *g1 = GenoObj::fromObject(args[1]);
        Geno *g2 = GenoObj::fromObject(args[0]);
        if (g1 == NULL || g2 == NULL)
                ret->setEmpty();
        else
                *ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(crossOver(*g1, *g2)));
}